Multiple Sclerosis (MS) is an autoimmune disorder of the central nervous system typified by axonal demyelination and neuronal death. To date, there is no effective treatment to cure the disease, and the available therapies do not alter the outcome of the disease. The development of better therapeutic options requires in-depth understanding of the molecular mechanisms leading to disease development and progression. Our group previously discovered a single nucleotide polymorphism (SNP, rs6897932) within exon 6 of the IL-7 receptor alpha chain (IL7R) that is strongly associated with the risk of developing MS. Our group further showed that the MS-associated allele of the SNP increases skipping of exon 6 both in vitro and in vivo, leading to increased production of a secreted receptor (sIL7R) that is unable to activate the IL-7 signaling pathway. Importantly, sIL7R has been linked to the disease in both human patients and animal models. These results directly implicate splicing of IL7R to the pathogenesis of MS, and posit the trans-acting factors controlling its splicing as candidate MS susceptibility genes. I have uncovered two of the trans-factors controlling IL7R exon 6 splicing: the RNA helicase DDX39B, which activates exon inclusion, and the polypyrimidine tract binding protein (PTBP1), which represses it. Furthermore, we uncovered several SNPs in the DDX39B gene region that are associated with MS, thereby establishing DDX39B is itself a risk factor for MS. None of the associated SNPs are located within the coding sequence of the gene, suggesting that one or more of these SNPs may contribute to the disease association by modifying DDX39B expression. Through bioinformatics and gene expression analyses, I have uncovered mRNA isoforms encoding either the full-length protein or a novel short protein, and several mRNA isoforms that are candidate targets for nonsense-mediated decay. Importantly, I have established two of the SNPs could alter expression levels of these isoforms. The goal of this proposal is to provide functional links connecting DDX39B to the pathogenesis of MS. Specifically, I aim to: 1) elucidate its role in the regulation of IL7R exon 6 splicing; 2) understand the functional roles of the different protein isoforms; and 3) uncover the SNPs responsible for its association with MS. I will combine biochemical and genetic approaches to elucidate the mechanism by which DDX39B activates exon 6 splicing, and to characterize the functional roles of the protein isoforms. I will test the impact of selected SNPs on DDX39B expression by combining in vivo gene expression analysis and functional studies using reporter minigenes. Successful completion of this research will advance our current understanding of the molecular underpinnings of MS, in particular by functionally linking DDX39B to the pathogenesis of MS, and providing a functional characterization of the DDX39B gene. Given that DDX39B has been associated with numerous autoimmune disorders, our results could be relevant to the mechanistic etiology of other autoimmune diseases.